GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PriCT_1 - Primase C terminal 1 (PriCT-1)
Pfam: PF08708 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Length: 71
Sequences: 436
Seq/Len: 6.14
HH_delta: 0.852 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
20_A42_A0.496463.091
13_N57_E0.446252.779
46_N53_L0.35132.187
17_F21_R0.34782.166
39_L59_K0.301781.879
16_L58_V0.288321.795
20_A65_I0.275161.713
41_L45_I0.240951.500
39_L62_A0.238231.483
56_S60_A0.231141.439
43_Q55_E0.223711.393
21_R24_A0.222351.385
40_S44_A0.212161.321
21_R68_W0.210911.313
55_E59_K0.209391.304
13_N61_I0.204261.272
17_F24_A0.20411.271
24_A68_W0.190161.184
11_G15_T0.184011.146
21_R65_I0.179981.121
43_Q47_S0.17851.111
18_R21_R0.175391.092
17_F65_I0.173621.081
7_I49_F0.169141.053
9_E51_P0.168051.046
63_K67_K0.164981.027
45_I48_N0.161841.008
6_G50_S0.156550.975
11_G14_C0.155320.967
14_C18_R0.152690.951
7_I45_I0.152060.947
17_F25_Y0.148680.926
10_G23_L0.144910.902
31_E56_S0.143820.896
39_L55_E0.143780.895
54_P60_A0.143220.892
27_G32_E0.142860.890
39_L47_S0.142810.889
8_V11_G0.142750.889
16_L20_A0.141770.883
47_S50_S0.136010.847
6_G59_K0.135770.845
10_G13_N0.13520.842
14_C67_K0.135090.841
6_G19_L0.133910.834
22_R65_I0.132750.827
13_N64_S0.131980.822
40_S43_Q0.130640.813
49_F52_P0.130310.811
43_Q56_S0.129680.807
7_I10_G0.129140.804
21_R25_Y0.126820.790
50_S56_S0.125130.779
23_L27_G0.124650.776
55_E61_I0.12410.773
14_C68_W0.123920.772
58_V63_K0.122910.765
19_L23_L0.121990.760
62_A66_A0.121870.759
28_V61_I0.121560.757
22_R26_R0.121370.756
38_V46_N0.120910.753
32_E47_S0.120610.751
24_A66_A0.119510.744
13_N53_L0.118960.741
62_A65_I0.11880.740
39_L43_Q0.11730.730
56_S63_K0.114840.715
15_T39_L0.113690.708
58_V62_A0.112460.700
13_N52_P0.112370.700
20_A47_S0.112280.699
15_T68_W0.111710.696
24_A41_L0.111490.694
26_R45_I0.111470.694
17_F68_W0.1110.691
42_A65_I0.110360.687
19_L22_R0.110160.686
23_L32_E0.109480.682
46_N65_I0.108780.677
15_T49_F0.108280.674
44_A49_F0.108150.673
43_Q51_P0.107840.671
29_D56_S0.107360.668
23_L41_L0.106340.662
15_T38_V0.106190.661
44_A48_N0.105760.659
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
2rftA0.971824.80.852
4b4cA0.3944220.855
2xb0X0.33821.10.856
3gjxA0.901415.40.864
4f0hB0.450714.20.867
1vu2F0.873214.20.867
1w9cA0.985913.90.867
1bxnI0.450713.60.867
1bwvS0.450712.80.869
1wddS0.5493110.872
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